Hormone signals like auxin play a critical role controlling plant growth and development. Determining the mechanisms that regulate auxin distribution in cells and tissues is a vital step in understanding this hormone's role during plant development. Recent mathematical models have enabled us to understand the essential role that auxin influx and efflux carriers play in auxin transport in the Arabidopsis root tip (Band et al., Plant Cell 26(3):862-875, 2014; Grieneisen et al., Nature 449(7165):1008-1013, 2007; van den Berg et al., Development 143(18):3350-3362, 2016). In this chapter, we describe SimuPlant: The Virtual Root (SimuPlant, University of Nottingham. https://www.simuplant.org/ . Accessed 20 Sept 2019); an open source software suite, built using the OpenAlea (Pradal et al., Funct Plant Biol 35(10):751-760, 2008) framework, that is designed to simulate vertex-based models in real plant tissue geometries. We provide guidance on how to install SimuPlant, run 2D auxin transport models in the Arabidopsis root tip, manipulate parameters, and visualize model outputs.SimuPlant features a graphical user interface (GUI) designed to allow users with no programming experience to simulate auxin dynamics within the Arabidopsis root tip. Within the user interface, users of SimuPlant can select from a range of model assumptions and can choose to manipulate model and simulation parameter values. Users can then investigate how their choices affect the predicted distribution of auxin in the Arabidopsis root tip. The results of the model simulations are shown visually within the root geometry and can be exported and saved as PNG image files.

Thomas C. Schelling showed that global aggregation may occur, even if it does not correspond to agent preferences; thus, to some extent his model supported the view that segregation is unavoidable, whatever the tolerance is. The segregation landscape approach proposed in this paper is seriously weakening this hypothesis; here, we radically change the perspective and propose using the landscape metaphor to represent emergent segregated communities. A segregation landscape is a mapping from situated individuals into an extra dimension that represents the degree of segregation of everyone. This paper uncovers how to interpret hills and valleys, and whether these interpretations are congruent with the intuitive notion of frontier. Such a representation allows us to describe both the static properties of a segregation space and their impact on how information propagates between segregated communities. In order to assess the explanatory power of the landscape metaphor, we devise agent-based simulations. First, we establish the link between the micro-level quantified by individual tolerance and the macro-structure represented by the landscape, then we show how "geographic" properties impact the dynamical behavior on such a population landscape.

Auxin is a key regulator of plant growth and development. Within the root tip, auxin distribution plays a crucial role specifying developmental zones and coordinating tropic responses. Determining how the organ-scale auxin pattern is regulated at the cellular scale is essential to understanding how these processes are controlled. In this study, we developed an auxin transport model based on actual root cell geometries and carrier subcellular localizations. We tested model predictions using the DII-VENUS auxin sensor in conjunction with state-of-the-art segmentation tools. Our study revealed that auxin efflux carriers alone cannot create the pattern of auxin distribution at the root tip and that AUX1/LAX influx carriers are also required. We observed that AUX1 in lateral root cap (LRC) and elongating epidermal cells greatly enhance auxin's shootward flux, with this flux being predominantly through the LRC, entering the epidermal cells only as they enter the elongation zone. We conclude that the nonpolar AUX1/LAX influx carriers control which tissues have high auxin levels, whereas the polar PIN carriers control the direction of auxin transport within these tissues.

The relation between individuality and aggregation is an important topic in complex systems sciences, both aspects being facets of emergence. This topic has frequently been addressed by adopting a classical, individual versus population level perspective. Here, however, the frontiers that emerge in segregated communities are the focus; segregation is synonymous with the existence of frontiers that delineate and interface aggregates. A generic agent-based model is defined, with which we simulate communities located on grid and scale-free networked environments. Emerging frontiers are analyzed in terms of their relative occupancy, porosity, and permeability. Results emphasize that the frontier is highly sensitive to the topology of the environment, not only to the agent tolerance. These relations are clarified while addressing the topics of frontier robustness and the trade-off between its capacity to separate and allow exchange.

Scientific research is a vanguard domain of human activity. Researchers aim for a systematic, objective approach, but also for pushing forward the boundaries of knowledge through the use of ever-more advanced instruments and techniques. Computer simulations represent such scientific instruments, capable of harvesting information in response to questions beyond the scope of traditional experimental techniques. The benefits of using them must, however, be considered together with aspects that led to criticism and lack of confidence e.g. they are difficult to analyze and validate, assumptions are only partially managed. This thesis scopes down the vast domain of simulation-based research, to the use of agent-based simulations for studying complex systems. The use of structured argumentation in a scientific research context is studied as a means for addressing the core limitations of simulation-based research. The Goal Structuring Notation has been used effectively in its originating domain - Safety Critical Systems - in addressing similar problems to simulation-based research. Through the use of this notation, this research emphasizes the difficulty of expressing compelling arguments, even in journal publications; in addition, it propose a set of extensions to the notation in order to adapt it to the scientific discourse. Finally, it shows the implications of studying a model in a rigorous, exhaustive manner, over the claims that can be made through it.

Food fermentation has been practiced since prehistoric times and developed over the years with modification in substrates, processes and technologies. It is carried out by microbial cultures with techniques such as back slopping and enrichment, enhancing the organoleptic property, nutrient availability and storage life of food and in many cases contributing beneficial microbes to the diet of the consumer.The microorganisms involved in fermentation greatly vary according to the food product. One of the major groups of microbes used in traditional and industrial fermentation of cereals includes the lactic acid bacteria, many of which are known to have probiotic characteristics followed by yeast and mould. While dairy fermented foods have received attention as a source of probiotic microbes, those in non-dairy foods especially millets and cereal mixtures have not been documented. Traditional fermented foods of animal origin as well as other plant foods such as pulse, fruits and vegetables are also discussed. The review examines the presumptive probiotic bacteria found in non-dairy fermented foods around the globe.This review is an attempt to collate the scientific progress with respect to probiotics in millet fermented foods, particularly of Africa and Asia. India has the largest documented number of fermented foods followed by Korea especially made with cereals. These fermented foods containing presumptive probiotic microorganisms may serve as probiotic supplements that are affordable as opposed to expensive probiotic formulations.

Research based on computer simulations, especially that conducted through agent-based experimentation, is often criticised for not being a reliable source of information - the simulation software can hide errors or flawed designs that inherently bias results. Consequently, the academic community shows both enthusiasm and lack of trust for such approaches. In order to gain confidence is using engineered systems, domains such as Safety Critical Systems employ structured argumentation techniques as means of explicitly relating claims to evidence - in other words, requirements to deliverables. We argue here that structured argumentation should be used in the development and validation process of simulation-driven research. Making use of the Goal Structuring Notation, we provide insights into how more trustworthy outcomes can be obtained through argumentation-driven validation.

In a model driven software development paradigm, UML sequence diagrams are used for modeling the interaction view of the software. For an application with high demanding of dependability, formal verification and analysis need to be performed on the sequence diagrams. This is usually done by transforming the sequence diagrams to a well studied formalism that has effective tool support to verification and analysis. In this paper, we propose an approach for transformations from sequence diagrams to CSP processes. The transformations are implemented by using the model driven software engineering standards, such as MOF, QVT, and XSLT. For this, we design the metamodels for sequence diagrams and CSP, and a set of transformation rules are specified using the QVT graphical syntax. The transformation rules are implemented as XSLT rule-based style templates. An XSLT engine reads the XMI file of a sequence diagram produced by an UML CASE tool, and then executes the XSLT templates, outputs the CSP model as an XML file. The XML file of the CSP processes can be translated into the input of a CSP checker for verification.

. Complex systems are often simulated to provide a basis for research or analysis. However, complex systems simulation often fails to properly demonstrate that the constructed simulation is an adequate tool to support investigation of the system under study. To address this issue we adopt and adapt argumentation techniques traditionally used for safety critical systems (SCS). Here we present part of an on-going case-study in which these techniques are used to demonstrate that two different implementations of a complex system simulation are adequately equivalent. This is a first step in producing further simulations of the system under study, which will be shown to be valid models on which to explore particular ecological phenomena.